


Then Came A Baby Boy...

by overcastskeleton



Series: IronStrange Library [7]
Category: Doctor Strange (2016), Iron Man (Movies), Marvel Cinematic Universe
Genre: Baby! Peter, Comedy, Domestic Fluff, Fatherhood, IronStrange, Magicfamily, Multi, Secret Relationship, Superfamily, Undercover, alternative universe, slight angst
Language: English
Status: In-Progress
Published: 2018-07-14
Updated: 2018-08-27
Packaged: 2019-06-10 08:13:15
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 3,176
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/15287433
Author URL: https://archiveofourown.org/users/overcastskeleton/pseuds/overcastskeleton
Summary: "Your mission, should you choose to accept it, is fatherhood."





	1. The Mission

**Author's Note:**

> I will be adding tags, characters and ships as they become relevant to the story
> 
> I'm really excited for this fic, and I hope you enjoy it!

Legacy.

Tony thought a lot about that word nowadays. If you were to ask him what his legacy would be 28 years ago, he would most likely say his weapons, Stark Industries, maybe his playboy title. Ask him ten years ago, he would say his “avenging.”

Ask him today, and he wouldn’t say either. See Tony never really had a reason to care about his legacy- until now.

It started the day Nick Fury showed up on his doorstep at five in the morning with a mission that would change his life forever.

**+++++++**

Tony woke up that morning to loud, erratic pounding on his front door.

He groaned and so did the body underneath him.

“Who the hell?” Tony questioned, rolling onto his side to look at his cellphone. “Five in the fucking morning?”

The pounding continued and Tony sat up. “I’m going to kill whoever that is.”

“Allow me to assist,” his boyfriend, Stephen, mumbled, sitting up beside him.

Tony rubbed his eyes and threw the blanket off of his legs. “I’m gonna see who’s trying to break down my door.” Tony kissed Stephen’s cheek. “Stay here.”

“Not a chance.” Stephen slipped his sling ring on with shaky fingers.

Tony rolled out of bed. “What if it’s somebody we know? They’re gonna ask a lot of questions when they see you here, shirtless, at five in the morning.”

“They’d be calling the kettle black,” Stephen said, but laid back down. “Yell if you need me.”

“I’ll be right back,” Tony said, stepping into the hallway.

The blue light from his arc reactor cast an eerie glow on the walls and made his shadow dance.

Tony summoned some armor to his hand as he reached the door. “Whoever you are, you better have a very good reason for waking me up at 5 A.M.” He aimed his blasters at the door.

“I assure you, Mr. Stark, this is very important,” came a familiar voice.

Tony peered through the peephole. “Fury?”

“The one and only,” Nick Fury replied. “Let me in, Stark. We need to talk.”

Tony unlocked the door reluctantly.

Director Nicholas J. Fury stood on his doorstep, arms crossed. “You better call your boyfriend, this issue concerns you both.”

“I’m here.” Stephen walked around the corner, his cloak floating silently behind him.  

Tony’s mouth dropped open. “How did you- we’re not-”

“We’ve known for months,” Fury interrupted Tony’s sputtering. “Do me a favor and stick to your day job, you both would make terrible spies.”

Tony tried to make a smart remark, but Fury held up a hand.

“We can talk about this later. You’ve got a mission, and it’s a level Alpha.” Fury stepped to the side, revealing a baby carrier with a small child inside. “Tony, Stephen, meet your son, Peter Parker.”

Tony raised his eyebrows in confusion. “Uh, yeah. I didn’t make that. I haven’t done anything with a woman since Pepper, and unless Stephen is cheating on me-”

“Which I’m not,” Stephen interjected.

“Then that’s not our kid.”

“Yeah, well starting now, he is.” Fury picked up the car seat and walked past Tony. “Do you have any whiskey? It’s been a long night.”

Stephen pulled a bottle from the cabinet and a glass. He poured the amber liquid in, waiting for a signal from Fury to stop; that didn’t come until the glass was damn near full.

“What happened?” Stephen slid the glass over to Fury, who took a long drink before speaking.

“I just lost two of my best agents to H.Y.D.R.A., and Peter watched his parents die.” Fury rubbed his jaw. “And now, here I am sitting in Tony Stark’s kitchen and putting the fate of S.H.I.E.L.D. into the hands of two egotistical dickheads.”

“Fury please,” Stephen chastised lightly, a small smirk on his face. “There’s a child here.”  

Tony slid into the seat opposite of Fury. “I’m a little confused, what does the kid have to do with H.Y.D.R.A.?”

Nick pulled a file from thin air.

“Do I want to know where you were keeping that?” Tony asked.

“We don’t have time for your humor, Stark. This is important.” Nick opened the file and slid it across the table. “Richard and Mary Parker, were assigned to infiltrate H.Y.D.R.A. and observe the usage of the replicated Super Serum until an opportune time presented itself for them to steal it.”

Stephen sat beside Tony and handed him a mug of coffee. Tony smiled gratefully and leaned his head against Stephen’s shoulder.

“What did S.H.I.E.L.D. want with the serum?” Stephen asked, raising an eyebrow.

Fury leaned back. “Only to keep it out of the wrong hands.”

“I’m not buying that,” Tony chuckled.

“It’s the truth,” Fury said, a hard expression on his face. “Richard and Mary’s covers were blown,and H.Y.D.R.A. had them killed, but not before they managed to steal and hide the serum.”

Stephen leaned his head against his hands. “And you think that they’ll come after Peter, because he’s the key to finding it.”

“Exactly,” Fury nodded. “We just need time to figure it out.”

“And what does that have to do with us?” Tony asked, glaring at Fury over the rim of his mug.

Fury pushed two more folders across the table. “We need you two to go deep undercover and take care of Peter. These are your new aliases.”

“You want Tony and I to play house?” Stephen interpreted.

“We want you to protect Peter.” Fury held up his hands. “Just until we find the serum.”

“Yeah?” Tony asked. “Why us?”

Fury sighed, as if the words he was about to utter left a bitter taste in his mouth. “Your relationship, albeit secret, is the most stable and secure one on this team.”

“What about Clint, or Thor and Bruce?”

“Clint already has enough kids. And Thor and Bruce are still galaxy hopping. Besides, Thor’s brother is far too willing to commit murder, and an infant may be too stressful for Dr. Banner.” Fury said. “So, as much as I hate to admit it, you’re our only hope.”

Stephen and Tony looked at each other, holding a quick conversation with their eyes. They didn’t really trust Fury, or his excuse for wanting the serum. But if they took the mission, they could keep an eye on Fury, and Peter. They’d be included, trusted, it would give them a chance to figure it out.

Tony glanced at Peter, who was still sleeping, his pink eyelids fluttering. He was so tiny; Tony couldn’t believe that life so complex, could exist in something so small. He was fascinated to say the least, but couldn’t help feeling oddly protective of the little boy sleeping in front of him.

“We’ll do it,” Tony said, still staring at Peter.


	2. The Alias Game

**Notes for the Chapter:**

> I'm back a few days early, because I literally couldn't wait to share this with you guys. 
> 
> I hope you enjoy!

When Fury left an hour later, Tony and Stephen had new identities, a house in the suburbs and, much to both Tony and Stephen’s chagrin, a shiny new minivan.

Peter had woken up about thirty minutes before Fury left, and stared around the room lazily for the rest of the meeting.

“I suggest you two get a move on, you’ve got quite the drive and the movers arrive at ten.” Fury stood. “It’s purely for show, everything you needed was moved into the house last night.”

Tony looked at Stephen. “We’re driving? Why not just travel with a portal?”

“We’ve have to keep up pretenses,” Fury said, a hint of an apology in his tone. “After this, you don’t have to use the car.”

“I’ll be fine." Stephen waved off Tony’s concern. "Besides, I can’t open a portal somewhere I haven’t been. The only thing that matters right now is Peter’s safety. So, when can we leave?”

Fury pointed to Peter. “I would feed him first. He gets cranky when he’s hungry.”

Peter was indeed beginning to make fussy noises that were gradually getting louder as the minutes passed by.

“How the hell do we do that?” Tony asked.

“Check the bag,” Fury said. “I’ll check in, in a few hours. Do me a favor and try not to kill him.”

Stephen pulled Fury aside. “Why us? We have next to no experience with kids, let alone a baby. Why give us this mission?”

“Doctor, I think you’re more capable of handling this than you think.” Fury said. “Besides, if anything goes wrong, I’m only a phone call away.” He clapped Stephen on the shoulder, and let himself out of the apartment.

Tony set the diaper bag on the table and began rifling through it. Inside it were a few baby bottles with formula, a couple parenting books, a change of clothes, diapers, wipes, a pacifier and a stuffed lamb.

When Tony held the lamb up to examine it, Peter’s brown eyes lit up. “Ba-ba,” he squealed, reaching out for it.

“He speaks.” Tony chuckled and held the stuffed animal out to Peter, who grabbed it and clutched it to his chest. It seemed to placate him for the moment.

Stephen read the instructions on the side of the formula container and spooned the appropriate amount into the bottle. “Well, this has been an unusually eventful morning.” He poured water into the bottle and began shaking it.

“I get what you mean.” Tony leafed through one of the books. “Here I thought I’d wake up to a lazy blowjob, not Fury pounding on our door.”

Stephen undid the straps of Peter’s car seat. “Lucky for us, I spent a very small amount of time working with infants while helping a hospital in Mumbai when I was in high school.”

“I never pegged you for someone who liked kids.” Tony sat back and watched Stephen pick up Peter with ease.

“I wasn’t fond of them for a while, but I never hated them.” Stephen shrugged, and nudged the bottle towards Peter’s mouth. “I didn’t think I’d ever have them,” Stephen admitted, a soft grin on his face as Peter latched on. “But, I am a different man than I was a decade ago.”

Tony nodded. “Yeah, time changes a lot.”

“Do you want to hold him?” Stephen asked.

Tony froze, baby clothes dangling from his fingertips. “I um- I-” he stammered. “I don’t want to break him.”

Stephen chuckled and nudged Tony back into the chair. “All you have to do is cradle his head against the inside of your arm, and keep him at an upward angle while he drinks. He’ll do the rest.”

“O-ok.” Tony said, holding his arms stiffly.

Peter made a small squeak of protest as Stephen removed the bottle from his mouth. He made grabbing hands at the container, brown eyes narrowed.

Stephen gently laid Peter in Tony’s arms. The latter tensed up the moment Peter came in contact with him. “Relax,” Stephen chided and handed the bottle to Tony.

Tony guided the tip towards Peter’s mouth with shaky fingers. Peter looked up at him, annoyance clearly written on his features. He looked at Stephen as if to say _“Who is this guy?_ ” Peter reached for the bottle, deciding to take matters into his own hands and tugged it towards his mouth.

Tony let out a breath, as Peter’s body relaxed into his own.

“See.” Stephen rubbed Tony’s shoulder. “That wasn’t so bad.”

Peter’s eyes were already beginning to flutter shut as he reached the bottom of the bottle.

“Yeah,” Tony chuckled dryly. “Yeah, that wasn’t so bad.”

Stephen looked around Tony’s apartment. “Well, I think it’s time to trade expensive high-rise apartments for a quaint two-story home.”

Tony was staring at Peter, who was breathing deeply, stuffed lamb still clutched tightly to his chest. “There’s a sentence I never thought I would hear.”

Stephen stood behind Tony, resting his chin on Tony’s head. “You never thought about starting a family, not even with Pepper?”

“Once,” Tony admitted. “But then you came along, you little homewrecker,” he joked.

Stephen rolled his eyes. “I doubt we’ll need anything from this apartment, but if you want to take anything, let me know. I’m packing a bag. We’ll be out of here in ten minutes.”

“Well I doubt Fury bought any of our crazy sex toys,” Tony said jokingly.

A portal opened in front of him and Tony barely had any time to duck before a box of condoms was launched through. The movement startled Peter, who opened his eyes lazily and stared up at Tony grumpily.

Tony froze, waiting for Peter to cry or show any sign of pain or discomfort, but they never came. Instead, Peter grabbed one of Tony’s fingers in his tiny little fist, buried his face into Tony’s chest and fell back to sleep.

Tony was still staring at Peter in awe when Stephen walked back into the room, carrying a small bag over his shoulder.

“I think he likes me,” Tony said, a proud smile on his face.

Stephen only replied with a soft smile. Domesticity never looked so good.

**+++++++**

“Are you alright, Steph?” Tony asked, taking his gaze off the road momentarily to glance at his boyfriend.

Stephen’s face was pale, his mouth pressed into a thin line and his jaw clenched. He had one hand gripping Tony’s and the other holding his seat belt. “I’m fine,” he said quietly, squeezing Tony’s hand. “How’s Peter?”

Tony looked in the rear-view mirror. Peter’s eyes met his, and the kid smiled dopily, letting out a small shriek of happiness.

“I’d say he’s feeling pretty good,” Tony reported. “You know for being stuck in a car with two strangers just hours after watching his parents die.”

Stephen’s mouth crooked into a small smile. “That makes one of us.”

“You just need a distraction,” Tony suggested.

“Tony please, there’s a child in the backseat.” Stephen smirked.

Tony rolled his eyes. “As appealing as that option would be, I was thinking more along the lines of figuring out who the hell we’re supposed to be now.”

“Where are the envelopes?” Stephen asked.

Tony turned to him, eyes wide. “You didn’t bring them?”

“You had them last,” Stephen protested. “We’ve been on the road for two hours Tony!”

Tony grinned, taking his hand away from Stephen’s to point to the backseat. “I’m joking, they’re in the diaper bag.”

Stephen glared at Tony, eyes narrowed impossibly thin. “Dumbass,” he muttered under his breath, and reached for the duffle bag.

“You would have laughed if you weren’t so riled up.” Tony chuckled.

Stephen pulled the envelopes free. “I would have smacked you.”

Tony grabbed Stephen’s hand and pressed a kiss to his palm. Stephen pulled his hand free and smacked Tony lightly.

“Well now I have a witness to all the abuse I endure at your hands,” Tony joked lightly and looked back at Peter grinning.

Peter smiled toothlessly, clutching the stuffed lamb to his chest, and babbled.

Stephen smiled for the first time the entire car ride. “Shall we?” He held up the contents of one of the manilla envelopes.

“Let me have it.” Tony reached for the bag of dried fruit in the cupholder, and popped a few blueberries into his mouth.

Stephen’s eyes scanned over the page and he groaned. “Damn you, Fury.”

“What?” Tony raised an eyebrow.

“It’s my name.” Stephen ran a hand over his face. “Who approves these things?”

Tony chewed on some strawberries. “It can’t be that bad.”

“Ba!” Peter shouted from the backseat.

“See, the kid agrees.” Tony jerked his thumb in Peter’s direction. “We won’t laugh, we promise.”

Stephen sighed. “My alias is,” he paused, “Benedict Cumberbatch.”

Tony’s eyes went wide, as he let out a huge guffaw, which resulted in him choking on his snack. He slammed on the brakes, and swerved the car off the road.

“Tony!” Stephen shouted, smacking Tony’s back.  

“Bendylick Cricketbat?” Tony sputtered breathlessly between laughs. “Did they just smash a bunch of letters together?”

Stephen rolled his eyes. “That’s not even remotely close to what I said.” Stephen deadpanned.

Peter shrieked with laughter, kicking his feet wildly.   

“If you, a saint in Fury’s eyes, got stuck with that name, I would hate to see what he picked for me.” Tony said, finally coming to his senses. He wiped tears from his eyes.

“Your alias is Robert Downey Jr.” Stephen said. “Which I must say is considerably better.”

Tony began driving again. “Lucky me. What about the kid?”

“Tom.” Stephen read. “He’s adopted, so they didn’t give him a last name. I guess he could take either of ours.”

“Well, I don’t want the kid to hate me for the rest of his life, so I think we’ll stick with mine, Benchthis.” Tony grinned.

Stephen knew he would never live this down. He would be sure to give Fury a piece of his mind when he got a chance to talk to him. “It’s Benedict! You better get it right before we get to the house.”

“I think I’ll call you Ben.” Tony compromised.

“Should I call you Bob?” Stephen replied mockingly.

It was Tony’s turn to glare. “Only if you enjoy sleeping on the couch.”   

Stephen held up his hands. “Just testing the waters.”

“Anything else in there?” Tony asked.

Stephen rifled through it. “Backstories mostly. Apparently I’m from the U.K., and so is Tom. Our occupations- you’re a mechanic-”

“You better start working on that accent.”

“Our occupations,” Stephen seamlessly slipped into a British accent. “You’re a mechanic, you own a small shop in town.”  

Tony stared at him, his jaw slack. “How did you-”

“I’m a stay at home dad.” Stephen read in disbelief.

“Whoever set you up must really have it out for you,” Tony squeezed Stephen’s hand lightly.

Stephen looked through the contents of the second, smaller envelope. This one was empty, except for a pair of house keys and a lump at the bottom of it. Stephen tipped it into his hands, two identical silicone engagement rings, and a note.

“‘We knew the metal would mess with your hands.’” Stephen read.

“So Fury has a heart after all.” Tony eyed the rings warily.

Stephen shrugged, sensing the mood change. “It’s all part of the cover, right?” He slipped the band onto his left ring finger.

Tony nodded, putting his on in turn. They’d only been together for a few months, and had definitely not had THE conversation yet. Still, Tony couldn’t help but feel weird that their engagement was a sham, and the ring on Stephen’s finger- the love of his life and his soulmate- was a fake.  

Stephen put his hand to Tony’s face. “Will you do me the honor of becoming Mr. Robert Cumberbatch?” He joked, trying to lighten the mood.

It worked. “Absolutely fucking not.” Tony cracked a grin.

“Watch your language, _Robert_ , there are little ears present.” Stephen chastised lightly, leaning over to kiss Tony’s cheek lightly.

Tony flushed, turning his head slightly so Stephen couldn’t see the rouge on his cheeks.

Yeah, maybe he could get used to this.

**Notes for the Chapter:**

> So, my college semester has just started, my current schedule isn't too busy, but that's subject to change. That being said, updates might not be super frequent. I hope you all can bear with me as I find time around my schedule to write and update. 
> 
> Thank you all so much for reading!

**Author's Note:**

> Let me know what you think so far!
> 
> \- I have not abandoned this story, updates will resume September 1, 2018-


End file.
